Variant report

Variant	rs6690210
Chromosome Location	chr1:46164394-46164395
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:46164046-46165901	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:46152318..46155647-chr1:46160597..46165176,4	MCF-7	breast:
2	chr1:46161054..46163559-chr1:46163619..46166713,3	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPBP1L1-1	chr1:46164119-46165067	NONHSAT002967
2	lnc-TMEM69-1	chr1:46164119-46165067	ENSG00000251202

No data

Variant related genes	Relation type
IPP	TF binding region
ENSG00000230896	TF binding region
ENSG00000230896	Chromatin interaction
ENSG00000159592	Chromatin interaction
ENSG00000159596	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11211148	1.00[YRI][hapmap]
rs11211150	1.00[YRI][hapmap]
rs11211153	1.00[YRI][hapmap]
rs11211154	1.00[YRI][hapmap]
rs11211155	1.00[YRI][hapmap]
rs12057167	1.00[YRI][hapmap]
rs12070177	1.00[YRI][hapmap]
rs12077112	1.00[YRI][hapmap]
rs12088810	1.00[YRI][hapmap]
rs12091360	1.00[YRI][hapmap]
rs12094011	1.00[YRI][hapmap]
rs28576912	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
2	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
3	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
4	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
5	nsv1011587	chr1:46051672-46244492	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv1014128	chr1:46097670-46394540	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
7	nsv1010054	chr1:46144479-46320493	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
8	nsv1006861	chr1:46144479-46417621	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
9	nsv1003049	chr1:46144479-46476149	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
10	nsv870511	chr1:46148138-46245423	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
11	nsv871233	chr1:46153203-46311275	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
12	nsv1008219	chr1:46160098-46493958	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
13	nsv534943	chr1:46160098-46493958	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6690210	HYI	cis	parietal	SCAN
rs6690210	HPDL	cis	parietal	SCAN
rs6690210	NSUN4	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46154600-46169400	Weak transcription	Ovary	ovary
2	chr1:46154600-46177200	Weak transcription	Aorta	Aorta
3	chr1:46154600-46180000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:46154600-46188600	Weak transcription	Fetal Heart	heart
5	chr1:46154600-46206600	Weak transcription	Brain Substantia Nigra	brain
6	chr1:46154800-46186000	Weak transcription	Psoas Muscle	Psoas
7	chr1:46154800-46192600	Weak transcription	Pancreas	Pancrea
8	chr1:46155000-46185200	Weak transcription	Colonic Mucosa	Colon
9	chr1:46155000-46187000	Weak transcription	NHLF	lung
10	chr1:46155000-46215800	Weak transcription	Small Intestine	intestine
11	chr1:46155200-46177600	Weak transcription	Fetal Brain Male	brain
12	chr1:46155200-46178800	Weak transcription	Stomach Mucosa	stomach
13	chr1:46155600-46204600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr1:46155800-46188400	Weak transcription	Hela-S3	cervix
15	chr1:46155800-46215600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr1:46156000-46177200	Weak transcription	Lung	lung
17	chr1:46156200-46170600	Weak transcription	HepG2	liver
18	chr1:46156600-46165400	Strong transcription	Fetal Intestine Large	intestine
19	chr1:46156600-46165800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:46156600-46165800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr1:46156800-46203800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr1:46157000-46164600	Weak transcription	Primary B cells from cord blood	blood
23	chr1:46157000-46166000	Strong transcription	Liver	Liver
24	chr1:46157200-46165600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:46157400-46173600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr1:46157400-46209800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr1:46158800-46165800	Strong transcription	Fetal Stomach	stomach
28	chr1:46159400-46165400	Weak transcription	K562	blood
29	chr1:46159400-46174200	Weak transcription	Esophagus	oesophagus
30	chr1:46159400-46176800	Weak transcription	Gastric	stomach
31	chr1:46159800-46173400	Weak transcription	A549	lung
32	chr1:46159800-46186800	Weak transcription	HSMMtube	muscle
33	chr1:46159800-46188000	Weak transcription	Right Ventricle	heart
34	chr1:46159800-46194800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr1:46160400-46165000	Strong transcription	Fetal Intestine Small	intestine
36	chr1:46160400-46180000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:46160400-46186800	Weak transcription	NH-A	brain
38	chr1:46160600-46174400	Weak transcription	Brain Angular Gyrus	brain
39	chr1:46160600-46188600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr1:46160800-46165200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr1:46160800-46173800	Weak transcription	Thymus	Thymus
42	chr1:46160800-46177000	Weak transcription	Fetal Kidney	kidney
43	chr1:46160800-46178400	Weak transcription	HUVEC	blood vessel
44	chr1:46160800-46179000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr1:46160800-46215400	Weak transcription	Brain Hippocampus Middle	brain
46	chr1:46161000-46165200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:46161000-46165400	Weak transcription	Rectal Smooth Muscle	rectum
48	chr1:46161000-46170400	Weak transcription	Left Ventricle	heart
49	chr1:46161000-46172000	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr1:46161000-46173400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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